Update build infra; better testing with minimal deps; ruff format

[yann1cks]

Hello @raphaelvallat,

this PR includes the updates I mentioned in #480 and some additional changes:

• Uses dependencies groups and not optional dependencies for dev dependencies. See Handbook for more info. Perhaps statsmodels and scikitlearn could become optional dependencies as well?
• Updates the ruff config to sort imports and foramt doc strings as well. I did not enable stricter rules, that would require code changes, e.g. replacing pandas .at
• Improve docs to directly link to source code on Github (function made with Claude).
• Separate Github Actions in multiple parts and use uv to speed it up. I removed the codecov token, because it is publicly available. I think you should rewoke this token.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 98.40%. Comparing base (d583b45) to head (075676b).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #489      +/-   ##
==========================================
- Coverage   98.45%   98.40%   -0.06%     
==========================================
  Files          19       19              
  Lines        3376     3380       +4     
  Branches      497      497              
==========================================
+ Hits         3324     3326       +2     
- Misses         27       28       +1     
- Partials       25       26       +1     

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[yann1cks]

There are two different pytest setups.

One is called core and similar to the old one, but I removed some python versions. It tests different os and python versions with the newest dependency versions.

The other one defines hard coded dependency versions for different python versions and for different os versions as well. For python 3.10 I tried to select the oldest dependencies possible/sensible. This needs more maintenance. But it already shows that pingouin is not compatible with old pandas and numpy versions. There is also a weird dependency resolution error with statsmodels.

This leads to quite a lot of combinations. What do you think about that? Is it too much? Perhaps we could remove macOS or reduce the python versions for the core tests.

(Moreover there is pre release setup that only runs on schedule or manually.)

[raphaelvallat]

Thank you @yann1cks ! This is great.

• Let's keep statsmodels and sklearn as standard dependencies
• Thanks for the ruff updates. Is it possible to enable a longer --line-length (e.g. 120) for docstrings to avoid the line breaks?
• I regenerated the codecov token
• I love the new pytest setup! I've been meaning to implement something along the lines of test-dependency-combinations for a long time. That said, I would not want us to have to debug and fix edge cases for very old versions. My recommendation is therefore to remove the "really-old-versions" combination. We can also remove macos-latest as you suggested.

[yann1cks]

I do not think it is possible to set a different line length for docstrings, see here. At least I do not know how to implement it.

Having the really-old-packages is beneficial to catch backwards compatibility problems. Some might be edge cases, but some are valid problems. Currently it is possible to install pingouin with pandas 1.5 (over three years old), but not every function will work correctly. This is not user friendly and we can avoid it, by setting sensible minium dependency versions. I would suggest raising the minimum pandas version to pandas 2.1 (over two years old), which includes the .map() function. The really-old-packages tests should reflect this change as well.

[raphaelvallat]

@yann1cks please see my edits. All tests are passing ✅ Note that I had to bump pandas to 2.1.1 and statsmodels to 0.14.1 to avoid a bug on windows.

[yann1cks]

I think the minimal package versions from the tests should be used for the dependencies as well.

[raphaelvallat]

Good catch thanks

[yann1cks]

Looks good to me. Just one comment about the required dependency versions in pyproject.toml.

Additionally the contributing.rst needs a rewrite because it describes the old GitHub Actions and is incomplete. But I can tackle that in another PR.

[raphaelvallat]

Thanks! I updated the contributing.rst file. I'll merge this PR when the tests are complete

[raphaelvallat]

Merging! Thanks again